if the GPU is somehow defective and forcing a lower frequency I'm not sure how to verify that other than test a different video card with similar (or better) specs (NVidia only as AMD DX11 drivers use more CPU cycles)
If you overclocked the GPU, put it back to the settings it originally came with.
I doubt this will help but try anyway:
1) download latest driver from NVidia
2) start install then choose "custom-> Clean" install path
Other:
a) you should have 8GB of DDR3 memory or more (at 4GB you may max out the system memory thus force swapping to the game HDD or SSD)
b) update BIOS to latest (v1403)
c) Memtest86 for a full pass www.memtest86.com (should not be directly behind your FPS issue)
d) make sure there is no WEB BROWSER open, and CPU isn't using much more than 10% (Task Manager) when loading the game. Again, you can alt-tab out and see if any of the cores get a big speak to 100% at the time of the big FPS drop
e) verify at least 3GB available in system memory for most games (Skyrim for me maxed at 1.75GB but some use over 3GB)
f) reinstalling Windows would be a last resort. If you don't have Windows 10 then I'd do that anyway. When I jumped from W7 to W8.1 I got an improvement due to CPU management in a couple games. On average there's little difference between W7/8/10 for gaming performance.
There could be however some software issue that is fixed by a clean OS install.
You likely have STEAM and note that you can reinstall it without redownloading all your games:
- keep the STEAMAPPS folder (so need at least two partitions on same drive or more than one drive)
- save Documents folder (to copy games save over for those with no CLOUD support), write down programs to reinstall, copy any passwords etc.
- W10 install media (MS media creation tool.. google for site and create DVD or USB if you have no W10 installation media)
- shut down, and unhook non-OS drives
- make sure BIOS is using UEFI (not compatibility/legacy settings)
- start W10 install
- DELETE everything so drive is blank if it was not partitioned
- when prompted for a key SKIP that
- finish all Microsoft Updates (Start-> Settings-> update.. let finish updates)
- install latest NVidia driver even if W10 appeared to install it
- install Steam to C-drive (ignore other programs until test)
- if you use a different drive use that folder (see Steam library settings... such as E:\Steam2), though the main Steam installation should be the OS drive even if you run no games on that drive
- sign in, then MOVE your Steamapps folder to replace the one in the new folder, reboot
- verify a game's local content then run it. (single player is more consistent to test than multiplayer, and preferably one with frequent stutter normally)
- test it and several other games and benchmarks
- finish install of other programs, setup fan profile if applicable etc